Evidence map›Paper›PMID 29458327›Full record

ArticleBMC genomics2018

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes.

Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L Allton, Dana Richardson, Jing Li, Hector L Franco, Anusha Nagari, Venkat S Malladi and 10 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
58citing papers in PubMed, 2 pooled it
3.6field-weighted citation impact, top 6% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

58 citing papers in PubMed, 2 syntheses or guidelines pooled it, 88 citations in OpenAlex.

  1. Pooled it
  2. Roles of AFAP1-AS1 in Gynecology and Urogenital System.Current pharmaceutical design · 2024
    Pooled it
  3. Article
  4. Article
  5. Review
  6. Article
  7. The role of epigenetic alterations in canine mammary cancer.The Journal of reproduction and development · 2026
    Review
  8. Article
  9. Article
  10. Article
  11. Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  12. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors at 3 institutions in 1 country.

Yuanxin XiDepartment of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA.
Jiejun ShiDepartment of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA.
Wenqian LiThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Kaori TanakaThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Kendra L AlltonThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Dana RichardsonThe Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Jing LiThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Hector L FrancoLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
Anusha NagariLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
Venkat S MalladiLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
Luis Della ColettaThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Melissa S SimperThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Khandan KeyomarsiThe Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
Jianjun ShenThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Mark T BedfordThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Xiaobing ShiThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
Michelle C BartonThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.
W Lee KrausLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
Wei LiDepartment of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA.
Sharon Y R DentThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA. sroth@mdanderson.org.ORCID http://orcid.org/0000-0002-4824-3269
The University of Texas MD Anderson Cancer Center · USThe University of Texas Southwestern Medical Center · USBaylor College of Medicine · US

Funding

Dose-Dependent Effects of Hormone on the Activity of Estrogen Receptor Enhancers and Target GenesR01DK058110 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI WILLIAM Lee KRAUS · 2000 to 2026
$10.4M
Cancer Prevention and Research Institute of Texas RP100417Cancer Prevention and Research Institute of Texas RP120348NIDDK NIH HHS R01 DK058110
6 · The paper itself

Abstract

backgroundEpigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy.

resultsTo define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells. DISCUSSION: Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway.

conclusionsTogether, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment.

Indexed as

Epigenesis, GeneticGene Expression Regulation, NeoplasticBiomarkers, TumorBreast NeoplasmsCell Line, TumorChromatinFemaleGene Expression ProfilingHistonesHumansTranscriptomeBiomarkers, TumorChromatinHistonesBreast cancer subtypesChromatin statesEpigeneticsHistone modifications

Identifiers

PMID29458327
PMCPMC5819162
OpenAlexW2788248735

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.